New flaxseed cultivars differing in seed mucilage content (MC) with low hull content (HC) represent an attractive option to simultaneously target the food and feed markets. Here, a genome-wide association study (GWAS) was conducted for MC and HC in 200 diverse flaxseed accessions genotyped with 1.7 million single nucleotide polymorphism (SNP) markers. The data obtained for MC and HC indicated a broad phenotypic variation and high (~70%) and a moderate (~49%) narrow sense heritability, respectively. MC and HC did not differ statistically between fiber and oil morphotypes, but yellow-seeded accessions had 2.7% less HC than brown-seeded ones. The genome-wide linkage disequilibrium (LD) decayed to r2 = 0.1 at a physical distance of ~100 kb. Seven and four quantitative trait loci (QTL) were identified for MC and HC, respectively. Promising candidate genes identified include Linum usitatissimum orthologs of the Arabidopsis thaliana genes TRANSPARENT TESTA 8, SUBTILISIN-LIKE SERINE PROTEASE, GALACTUROSYL TRANSFERASE-LIKE 5, MUCILAGE-MODIFIED 4, AGAMOUS-LIKE MADS-BOX PROTEIN AGL62, GLYCOSYL HYDROLASE FAMILY 17, and UDP-GLUCOSE FLAVONOL 3-O-GLUCOSYLTRANSFERASE. These genes have been shown to play a role in mucilage synthesis and release, seed coat development and anthocyanin biosynthesis in A. thaliana. The favorable alleles will be useful in flaxseed breeding towards the goal of achieving the ideal MC and HC composition for food and feed by genomic-based breeding.

Linseed (Linum usitatissimum L.) is well known for containing functional compounds with health‐related benefits. Assessed were the agronomic and seed‐quality traits of 13 linseed advanced breeding lines (ABLs) varying in seed mucilage content (SMC) that could be better suited to Chilean environments and food and feed market needs. Analysis of variance revealed highly significant genotype and environment effects for most of the traits assessed. Seed mucilage content ranged from 0.89 to 5.45%, and various ABLs exhibited similar yield and yield‐related traits to the controls, but some outperformed them for harvest index, plant height, and days to 5% flowering. The yellow‐seeded ABLs showed the highest and lowest oil and hull content, respectively, as compared with the brown‐seeded lines. The majority of the ABLs exhibited high linolenic acid content, ∼60%. The four most promising ABLs were further characterized for the content of the cyanogenic glycosides (CGs) linustatin and neolinustatin, where LuCGNA11 and LuCGNA67 had the lowest values for both CGs. We evaluated the effects of two ABLs contrasting in SMC on laying hen weight (control = 1794 g), egg production (control = 117 eggs), and egg weight (control = 62.9 g) over a 4‐wk period. Hens fed the low SMC diet had an increase of 78.6 g, 13 eggs, and 3.86 g, while the high SMC diet had a reduction of 36.8 g, 25 eggs, and 2.8 g for body weight, egg production, and egg weight, respectively. These new high and low SMC ABLs offer opportunities to the food and feed industry for the generation of new value‐added products.

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New flaxseed cultivars differing in seed mucilage content (MC) with low hull content (HC) represent an attractive option to simultaneously target the food and feed markets. Here, a genome-wide association study (GWAS) was conducted for MC and HC in 200 diverse flaxseed accessions genotyped with 1.7 million SNP markers. The data obtained for MC and HC indicated a broad phenotypic variation and high (~70%) and a moderate (~49%) narrow sense heritability, respectively. MC and HC did not differ statistically between fiber and oil morphotypes, but yellow-seeded accessions had 2.7% less HC than brown-seeded ones. The genome wide linkage disequilibrium (LD) decayed to r2 = 0.1 at a physical distance of ~100 Kb. Seven and four QTL were identified for MC and HC, respectively. Promising candidate genes included Linum usitatissimum orthologs of the Arabidopsis thaliana genes TRANSPARENT TESTA 8, SUBTILISIN-LIKE SERINE PROTEASE, GALACTUROSYL TRANSFERASE-LIKE 5, MUCILAGE-MODIFIED 4, AGAMOUS-LIKE MADS-BOX PROTEIN AGL62, GLYCOSYL HYDROLASE FAMILY 17 and UDP-GLUCOSE FLAVONOL 3-O-GLUCOSYLTRANSFERASE that have been shown to play a role in mucilage synthesis and release, seed coat development and anthocyanin biosynthesis in A. thaliana were identified. The favorable alleles will be useful in flaxseed breeding towards the goal of achieving the ideal flaxseed cultivars for food and feed by genomic-based breeding.